Magnesium in PDB 1sjb: X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid

The structure of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid, PDB code: 1sjb was solved by J.B.Thoden, E.A.Taylor-Ringia, J.B.Garrett, J.A.Gerlt, H.M.Holden, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	216.000, 216.000, 261.000, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid (pdb code 1sjb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid, PDB code: 1sjb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:50.0 occ:1.00 O2 A:OSB1000 1.8 79.1 1.0 O A:HOH1116 2.0 35.6 1.0 OD2 A:ASP239 2.5 34.3 1.0 OE2 A:GLU214 2.5 49.4 1.0 OD2 A:ASP189 2.5 37.4 1.0 C7 A:OSB1000 2.9 55.9 1.0 CD A:GLU214 3.0 60.5 1.0 CG A:ASP189 3.1 42.5 1.0 O1 A:OSB1000 3.3 65.0 1.0 OD1 A:ASP189 3.3 36.6 1.0 CG A:ASP239 3.5 36.4 1.0 CB A:ASP239 3.6 32.7 1.0 ND2 A:ASN191 3.6 43.5 1.0 OE1 A:GLU214 3.6 60.7 1.0 CG A:GLU214 3.7 36.5 1.0 OE1 A:GLU240 3.8 46.7 1.0 NZ A:LYS161 3.9 49.5 1.0 C2 A:OSB1000 4.1 44.9 1.0 NZ A:LYS263 4.1 37.5 1.0 CG A:ASN191 4.3 56.7 1.0 CB A:ASP189 4.4 26.8 1.0 C3 A:OSB1000 4.4 0.0 1.0 ND2 A:ASN261 4.5 31.6 1.0 OD1 A:ASN191 4.5 39.6 1.0 CE A:LYS263 4.5 32.7 1.0 CB A:GLU214 4.5 34.6 1.0 OD1 A:ASP239 4.6 48.5 1.0 CD A:GLU240 4.7 28.0 1.0 CE A:LYS161 4.8 32.8 1.0 OE2 A:GLU240 4.9 26.1 1.0 CE2 A:TYR55 5.0 49.5 1.0

Magnesium binding site 2 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1101 b:45.0 occ:1.00 OE2 B:GLU214 2.0 61.6 1.0 O2 B:OSB1100 2.2 52.2 1.0 O B:HOH1276 2.4 27.8 1.0 OD2 B:ASP239 2.4 25.5 1.0 OD2 B:ASP189 2.6 32.1 1.0 CD B:GLU214 2.7 33.9 1.0 C7 B:OSB1100 3.1 36.3 1.0 O1 B:OSB1100 3.2 54.9 1.0 CG B:ASP189 3.2 32.7 1.0 OE1 B:GLU214 3.3 41.1 1.0 OD1 B:ASP189 3.3 28.2 1.0 NZ B:LYS161 3.5 31.1 1.0 CG B:GLU214 3.5 25.1 1.0 CG B:ASP239 3.6 42.1 1.0 NZ B:LYS263 3.7 37.7 1.0 CB B:ASP239 3.8 23.2 1.0 ND2 B:ASN191 3.9 50.9 1.0 ND2 B:ASN261 4.0 26.4 1.0 C2 B:OSB1100 4.4 38.7 1.0 OE1 B:GLU240 4.5 32.4 1.0 CB B:ASP189 4.5 28.1 1.0 CE B:LYS161 4.6 46.8 1.0 CB B:GLU214 4.6 29.5 1.0 OD1 B:ASP239 4.6 28.7 1.0 CE B:LYS263 4.6 42.9 1.0 NZ B:LYS163 4.7 43.0 1.0 CG B:ASN191 4.7 40.6 1.0 OD1 B:ASN191 4.9 22.9 1.0 C3 B:OSB1100 4.9 25.9 1.0 CG B:ASN261 5.0 33.5 1.0

Magnesium binding site 3 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1201 b:67.4 occ:1.00 OD2 C:ASP239 1.8 36.1 1.0 O2 C:OSB1200 2.0 51.3 1.0 O C:HOH1343 2.3 32.1 1.0 OE2 C:GLU214 2.4 39.1 1.0 OD2 C:ASP189 2.6 48.4 1.0 C7 C:OSB1200 2.9 77.1 1.0 CG C:ASP239 3.0 44.6 1.0 O1 C:OSB1200 3.1 39.3 1.0 ND2 C:ASN191 3.1 52.5 1.0 OD1 C:ASP189 3.2 36.6 1.0 CG C:ASP189 3.3 49.4 1.0 NZ C:LYS263 3.4 47.4 1.0 CD C:GLU214 3.5 34.1 1.0 CB C:ASP239 3.6 29.9 1.0 OE1 C:GLU240 3.9 31.2 1.0 OD1 C:ASP239 4.0 39.9 1.0 CG C:ASN191 4.1 44.2 1.0 NZ C:LYS161 4.1 55.2 1.0 OE1 C:GLU214 4.2 53.8 1.0 C2 C:OSB1200 4.2 52.8 1.0 CG C:GLU214 4.2 45.5 1.0 OD1 C:ASN191 4.4 38.6 1.0 CE2 C:TYR55 4.4 38.4 1.0 CE C:LYS263 4.4 28.2 1.0 OE2 C:GLU240 4.4 25.9 1.0 CD C:GLU240 4.5 34.5 1.0 C3 C:OSB1200 4.5 40.6 1.0 ND2 C:ASN261 4.7 29.9 1.0 CB C:ASP189 4.7 21.5 1.0 NZ C:LYS163 4.7 39.6 1.0 OH C:TYR55 4.9 38.9 1.0 CE C:LYS161 5.0 35.6 1.0

Magnesium binding site 4 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with O-Succinylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1301 b:69.6 occ:1.00 OD2 D:ASP239 1.8 40.5 1.0 O2 D:OSB1300 2.1 0.0 1.0 O D:HOH1411 2.3 51.9 1.0 OE2 D:GLU214 2.3 40.6 1.0 OD2 D:ASP189 2.8 36.4 1.0 C7 D:OSB1300 3.0 50.6 1.0 CG D:ASP239 3.1 52.5 1.0 CD D:GLU214 3.2 39.7 1.0 O1 D:OSB1300 3.2 0.0 1.0 NZ D:LYS263 3.4 41.2 1.0 ND2 D:ASN191 3.5 46.9 1.0 CB D:ASP239 3.6 44.8 1.0 CG D:ASP189 3.7 40.6 1.0 CG D:GLU214 3.8 34.9 1.0 OE1 D:GLU240 3.8 46.0 1.0 OD1 D:ASP189 3.9 34.2 1.0 NZ D:LYS161 3.9 58.2 1.0 OE1 D:GLU214 3.9 36.1 1.0 OD1 D:ASP239 4.0 41.2 1.0 CE D:LYS263 4.3 33.6 1.0 C2 D:OSB1300 4.3 0.0 1.0 CG D:ASN191 4.5 57.6 1.0 CE2 D:TYR55 4.5 43.5 1.0 ND2 D:ASN261 4.6 31.9 1.0 C3 D:OSB1300 4.7 74.4 1.0 CD D:GLU240 4.7 40.0 1.0 OD1 D:ASN191 4.7 30.9 1.0 NZ D:LYS163 4.8 43.8 1.0 CE D:LYS161 4.9 38.2 1.0 CB D:ASP189 4.9 18.3 1.0

J.B.Thoden, E.A.Taylor-Ringia, J.B.Garrett, J.A.Gerlt, H.M.Holden, I.Rayment. Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous O-Succinylbenzoate Synthase From Amycolatopsis Biochemistry V. 43 5716 2004.
ISSN: ISSN 0006-2960
PubMed: 15134446
DOI: 10.1021/BI0497897